Dataset: Relative protein abundance from scaled and corrected exclusive peptide spectral counts from the ProteOMZ R/V Falkor expedition cruise FK160115 in the Pelagic central Pacific Ocean in 2016

Final no updates expectedDOI: 10.26008/1912/bco-dmo.868030.1Version 1 (2022-01-13)Dataset Type:Cruise Results

Principal Investigator: Mak A. Saito (Woods Hole Oceanographic Institution)

Scientist: Jaci Saunders (Woods Hole Oceanographic Institution)

BCO-DMO Data Manager: Amber D. York (Woods Hole Oceanographic Institution)


Program: Marine Microbiology Initiative (MMI)

Project: The ProteOMZ Expedition: Investigating Life Without Oxygen in the Pacific Ocean (ProteOMZ (Proteomics in an Oxygen Minimum Zone))

Project: Marine Microbial Investigator Award: Investigator Mak Saito (MM Saito)


Abstract

Relative protein abundance from scaled and corrected exclusive peptide spectral counts from 20-1250 m in the water column (0.2-3 µm filter size fraction) from the ProteOMZ R/V Falkor expedition. There are a total of 107,579 unique peptide sequences from 56,543 protein groups (88,251 proteins). Exclusive spectral counts are provided per sample as are the full dataset scaled and normalized spectral counts. The protein distributions in this dataset highlight the microbial dynamics across biomes in ...

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Methods & Sampling:

Samples were handled as described in (Saunders et al., submitted) and (McIlvin et al., 2021). There are a total of 107,579 unique peptide sequences from 56,543 protein groups (88,251 proteins). Proteins were extracted from biomass collected on a quarter section of a 142 mm 0.2 µm Supor filter (Pall Corporation) after pre-filtration through a 3.0 µm Supor filter. Proteins were extracted using a modified SP3 magnetic bead method (Hughes et al., 2014). Extracted proteins were quatified using the bicinchoninic acid method (Thermo Scientific Micro BCA protein assay kit) with an albumin protein reference standard. Extracted protein was purified and digested with trypsin. Purified and digested protein was then injected into an online nanoflow 2D active modulation liquid chromatography separation (McIlvin et al., 2021). Eluent flowed inline into the ion source of a Thermo Fusion quadrupole-Orbitrap mass spectrometer (Thermo Scientific). MS/MS spectra (and mass spec methods) are available at the PRIDE repository under accession PXD030684. Peptide to spectrum matching (PSM) on the MS/MS data was conducted with SEQUEST HT using Thermo Proteome Discoverer v 2.1 software against a database of predicted proteins from an assembled metagenome from the central Pacific Ocean. Additional protein inference and FDR calculations were conducted with Scaffold v 4.8.7. Identification was conducted with decoy false discovery rates (FDR) with a threshold of 95% minimum for peptides (FDR=0.1%) and a threshold of 99% (1 peptide minimum) for proteins (FDR=1.6%). Protein level inference for parsimony-based assignments of specific proteins was conducted using experiment-wide grouping with binary peptide-protein weights in Scaffold. All PSM and protein quantification in Scaffold was conducted using Exclusive Counts (not double-counted, PSM assignment to protein groups using parsimony). 

Location: Pelagic central Pacific Ocean from 20 – 1250 m depth


Related Datasets

IsRelatedTo

Dataset: ProteOMZ identified protein sequences
Relationship Description: These datasets are part of the Ocean Protein Portal "ProteOMZ" dataset (https://proteinportal.whoi.edu/; Saito et al., 2019).
Saito, M. A. (2024) FASTA file of identified protein sequences from the R/V Falkor cruise 160115 for the ProteOMZ expedition in the Central Pacific during 2016. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 3) Version Date 2019-02-15 doi:10.26008/1912/bco-dmo.737611.3
IsRelatedTo

Dataset: ProteOMZ Protein Level Spectral Counts
Relationship Description: These datasets are part of the Ocean Protein Portal "ProteOMZ" dataset (https://proteinportal.whoi.edu/; Saito et al., 2019).
Saito, M. A. (2024) Total spectral count of proteins from R/V Falkor cruise 160115 for the ProteOMZ expedition in the Central Pacific in 2016. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 3) Version Date 2022-06-06 doi:10.26008/1912/bco-dmo.737620.3
IsRelatedTo

Dataset: R/V Falkor 160115 ProteOMZ Trace Metal Rosette Data
Relationship Description: This dataset was collected asynchronously using another instrument at the same stations during the expedition.
Saito, M. A., Santoro, A. E. (2018) Hydrographic data from the CTD mounted on the trace metal rosette (TMR) aboard R/V Falkor cruise (160115) during the ProteOMZ expedition in the Central Pacific in 2016. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2018-05-01 http://lod.bco-dmo.org/id/dataset/734608
IsRelatedTo

Dataset: ProteOMZ nutrient, CTD, and oxygen data
Relationship Description: This dataset was collected asynchronously using another instrument at the same stations during the expedition.
Saito, M. A., Santoro, A. E. (2018) Macronutrient analysis and selected hydrographic data from the R/V Falkor ProteOMZ expedition (FK160115) in the Central Pacific in 2016. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2018-11-19 http://lod.bco-dmo.org/id/dataset/730912
IsRelatedTo

Dataset: R/V Falkor 160115 ProteOMZ CTD information
Relationship Description: This dataset was collected asynchronously using another instrument at the same stations during the expedition.
Saito, M. A., Santoro, A. E. (2018) SeaBird SBE19 underway CTD information for the R/V Falkor 160115 cruise in the Central Pacific for the ProteOMZ expedition in 2016. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2018-06-15 http://lod.bco-dmo.org/id/dataset/730925

Related Publications

Results

Saunders, J. K., McIlvin, M. R., Dupont, C. L., Kaul, D., Moran, D. M., Horner, T., Laperriere, S. M., Webb, E. A., Bosak, T., Santoro, A. E., & Saito, M. A. (2022). Microbial functional diversity across biogeochemical provinces in the central Pacific Ocean. Proceedings of the National Academy of Sciences, 119(37). https://doi.org/10.1073/pnas.2200014119
Methods

Hughes, C. S., Foehr, S., Garfield, D. A., Furlong, E. E., Steinmetz, L. M., & Krijgsveld, J. (2014). Ultrasensitive proteome analysis using paramagnetic bead technology. Molecular Systems Biology, 10(10), 757. doi:10.15252/msb.20145625
Methods

McIlvin, M. R., & Saito, M. A. (2021). Online Nanoflow Two-Dimension Comprehensive Active Modulation Reversed Phase–Reversed Phase Liquid Chromatography High-Resolution Mass Spectrometry for Metaproteomics of Environmental and Microbiome Samples. Journal of Proteome Research, 20(9), 4589–4597. doi:10.1021/acs.jproteome.1c00588
Methods

Saunders, J. K., Gaylord, D. A., Held, N. A., Symmonds, N., Dupont, C. L., Shepherd, A., … Saito, M. A. (2020). METATRYP v 2.0: Metaproteomic Least Common Ancestor Analysis for Taxonomic Inference Using Specialized Sequence Assemblies—Standalone Software and Web Servers for Marine Microorganisms and Coronaviruses. Journal of Proteome Research, 19(11), 4718–4729. doi:10.1021/acs.jproteome.0c00385